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Basic information

Entry
Database: PDB / ID: 4oiz
TitleStructure, interactions and evolutionary implications of a domain-swapped lectin dimer from Mycobacterium smegmatis
ComponentsLysM domain protein
KeywordsSUGAR BINDING PROTEIN / Beta-prism II fold / Bacterial lectin / protein-carbohydrate interactions / Beta-Prism II / Carbohydrate binding / Carbohydrate/Sugar
Function / homology
Function and homology information


Agglutinin, subunit A / Bulb-type lectin domain / Bulb-type lectin domain / Bulb-type lectin domain superfamily / Bulb-type lectin domain profile. / Bulb-type mannose-specific lectin / Orthogonal Prism / Lysin motif / LysM domain superfamily / LysM domain ...Agglutinin, subunit A / Bulb-type lectin domain / Bulb-type lectin domain / Bulb-type lectin domain superfamily / Bulb-type lectin domain profile. / Bulb-type mannose-specific lectin / Orthogonal Prism / Lysin motif / LysM domain superfamily / LysM domain / LysM domain profile. / LysM domain / Mainly Beta
Similarity search - Domain/homology
methyl alpha-D-mannopyranoside / Mannose-binding lectin
Similarity search - Component
Biological speciesMycobacterium smegmatis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.4 Å
AuthorsPatra, D. / Mishra, P. / Surolia, A. / Vijayan, M.
Citation
Journal: Glycobiology / Year: 2014
Title: Structure, interactions and evolutionary implications of a domain-swapped lectin dimer from Mycobacterium smegmatis.
Authors: Patra, D. / Mishra, P. / Surolia, A. / Vijayan, M.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2011
Title: Cloning, expression, purification, crystallization and preliminary X-ray studies of the mannose-binding lectin domain of MSMEG_3662 from Mycobacterium smegmatis
Authors: Patra, D. / Sharma, A. / Chandran, D. / Vijayan, M.
#2: Journal: J.Biosci. / Year: 2007
Title: Multiplicity of carbohydrate-binding sites in beta-prism fold lectins: occurrence and possible evolutionary implications
Authors: Sharma, A. / Chandran, D. / Singh, D.D. / Vijayan, M.
#3: Journal: Proteins / Year: 2013
Title: Identification of mycobacterial lectins from genomic data
Authors: Abhinav, K.V. / Sharma, A. / Vijayan, M.
History
DepositionJan 20, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 23, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2Aug 24, 2022Group: Database references / Structure summary / Category: chem_comp / citation / database_2
Item: _chem_comp.pdbx_synonyms / _citation.journal_volume ..._chem_comp.pdbx_synonyms / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: LysM domain protein
B: LysM domain protein
C: LysM domain protein
D: LysM domain protein
E: LysM domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,87411
Polymers62,7095
Non-polymers1,1656
Water0
1
A: LysM domain protein
B: LysM domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,6665
Polymers25,0842
Non-polymers5833
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4830 Å2
ΔGint-37 kcal/mol
Surface area10470 Å2
MethodPISA
2
C: LysM domain protein
D: LysM domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,4724
Polymers25,0842
Non-polymers3882
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4830 Å2
ΔGint-38 kcal/mol
Surface area10320 Å2
MethodPISA
3
E: LysM domain protein
hetero molecules

E: LysM domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,4724
Polymers25,0842
Non-polymers3882
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area4920 Å2
ΔGint-39 kcal/mol
Surface area10350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)123.510, 80.860, 100.940
Angle α, β, γ (deg.)90.00, 130.69, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
LysM domain protein / / Mannose-binding lectin


Mass: 12541.867 Da / Num. of mol.: 5 / Fragment: mannose-binding lectin domain, UNP residues 1-105
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium smegmatis (bacteria) / Strain: MC2 155 / Gene: MSMEG_3662 / Plasmid: pET21b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0QYH7
#2: Sugar
ChemComp-MMA / methyl alpha-D-mannopyranoside / O1-METHYL-MANNOSE / methyl alpha-D-mannoside / methyl D-mannoside / methyl mannoside / Methylglucoside


Type: D-saccharide / Mass: 194.182 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Formula: C7H14O6
IdentifierTypeProgram
DManp[1Me]aCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
1-methyl-a-D-mannopyranoseCOMMON NAMEGMML 1.0
o1-methyl-mannoseIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.05 Å3/Da / Density % sol: 59.64 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 2.0M ammonium citrate tribasic, 0.1M bis-tris propane, 60mM methyl-alpha-mannose, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.54179 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jun 1, 2012 / Details: mirrors
RadiationMonochromator: Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54179 Å / Relative weight: 1
ReflectionResolution: 3.4→40 Å / Num. obs: 10344 / % possible obs: 98.4 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.156 / Net I/σ(I): 6
Reflection shellResolution: 3.4→3.58 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.43 / Num. unique all: 1500 / % possible all: 98.1

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
REFMAC5.8.0049refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Native structure

Resolution: 3.4→40 Å / Cor.coef. Fo:Fc: 0.906 / Cor.coef. Fo:Fc free: 0.863 / SU B: 91.775 / SU ML: 0.671 / Cross valid method: THROUGHOUT / ESU R Free: 0.641 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2882 494 4.8 %RANDOM
Rwork0.242 ---
obs0.2443 9835 98.26 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 137.38 Å2 / Biso mean: 75.581 Å2 / Biso min: 35.33 Å2
Baniso -1Baniso -2Baniso -3
1--3.23 Å20 Å2-4.56 Å2
2--2.52 Å2-0 Å2
3---3.45 Å2
Refinement stepCycle: LAST / Resolution: 3.4→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3951 0 78 0 4029
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.024094
X-RAY DIFFRACTIONr_bond_other_d0.0040.023809
X-RAY DIFFRACTIONr_angle_refined_deg0.7861.9645585
X-RAY DIFFRACTIONr_angle_other_deg0.66338736
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0765527
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.34525.81179
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.58315605
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.0941515
X-RAY DIFFRACTIONr_chiral_restr0.0520.2660
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.024735
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02902
X-RAY DIFFRACTIONr_mcbond_it0.3683.1512123
X-RAY DIFFRACTIONr_mcbond_other0.3683.1512122
X-RAY DIFFRACTIONr_mcangle_it0.6814.7222645
LS refinement shellResolution: 3.4→3.488 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.374 35 -
Rwork0.325 729 -
all-764 -
obs--97.7 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.0099-2.59230.75787.3411-2.59671.71930.03860.1058-0.24370.17750.14990.3909-0.1688-0.188-0.18850.4044-0.0844-0.3510.65320.00280.3911-22.9287-3.195210.363
21.906-2.18960.58598.4736-2.5030.75610.45930.316-0.1691-1.1029-0.5499-0.40870.33070.2410.09070.65840.1073-0.20030.7281-0.09580.1818-17.95160.48111.9885
32.8353-0.63062.31261.94090.44113.2488-0.2106-0.1188-0.08640.09810.50170.1146-0.65670.385-0.2910.4252-0.08230.09360.9157-0.04390.152723.6304-5.159938.165
41.1082-2.90741.03788.6462-4.2283.48080.24590.19340.1407-0.5448-0.2055-0.33790.08240.054-0.04040.2486-0.0421-0.14180.5433-0.00180.2448-0.01831.625425.5833
52.2185-3.05981.67546.2351-3.86732.4850.2443-0.0739-0.2054-0.15160.13650.53560.0857-0.1598-0.38070.3374-0.0001-0.1740.5206-0.06880.1698-9.46225.7327.6237
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1C2 - 106
2X-RAY DIFFRACTION2D2 - 106
3X-RAY DIFFRACTION3E2 - 106
4X-RAY DIFFRACTION4A2 - 106
5X-RAY DIFFRACTION5B2 - 106

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